BN1506 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 2.8562e-07 1.8633e-03
Layer 3 8.0051e-07 1.9002e-02
Layer 5 2.3527e-06 4.7660e-03
Layer 2 3.9831e-03 4.1370e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.0312 0.6760
PARM1 Layer 4 2.1719 0.6433
MPPED1 Layer 4 2.1074 0.6381
ITPK1 Layer 5 2.1191 0.6362
NUDT4 Layer 5 2.1348 0.6337
ATXN7L3B Layer 4 2.0078 0.6314
EVL Layer 5 2.0312 0.6311
STX1A Layer 5 2.1348 0.6274
GLRB Layer 4 2.1123 0.6270
SEPTIN8 Layer 4 1.9517 0.6269
KCNJ9 Layer 4 1.9541 0.6238
GALNT8 Layer 4 2.0332 0.6234
BRSK2 Layer 4 1.9990 0.6231
IGIP Layer 4 1.9453 0.6222
OAT Layer 4 1.9014 0.6220
SVOP Layer 5 2.0312 0.6203
FEM1B Layer 4 2.0146 0.6196
LRPAP1 Layer 4 2.1602 0.6193
PNMA8B Layer 5 2.0254 0.6183
ATP1B3 Layer 5 1.8545 0.6176
TTC19 Layer 5 1.8711 0.6166
PAM Layer 5 1.9805 0.6165
MAP6 Layer 5 1.9102 0.6163
GOT1 Layer 5 2.0488 0.6162
NEUROD2 Layer 5 2.0820 0.6151
APBA2 Layer 4 2.1250 0.6139
MCRIP1 Layer 4 2.0176 0.6126
CUEDC2 Layer 5 2.0176 0.6125
CCT7 Layer 4 1.9941 0.6113
LRRC47 Layer 4 1.8672 0.6107
PHF24 Layer 5 2.1484 0.6104
PRUNE2 Layer 5 2.2363 0.6095
ACOT7 Layer 4 2.0039 0.6090
OPCML Layer 5 1.8584 0.6079
SLC25A12 Layer 4 1.9805 0.6078
STRAP Layer 5 1.8799 0.6069
PTOV1 Layer 4 1.9854 0.6059
CDC37 Layer 4 2.0918 0.6053
ROGDI Layer 5 1.8926 0.6052
ELAVL4 Layer 5 2.0176 0.6045
ACVR1B Layer 5 1.8330 0.6042
GABRA5 Layer 5 2.2363 0.6035
CMAS Layer 4 1.8369 0.6033
SLC25A22 Layer 5 2.1914 0.6024
ERI3 Layer 5 1.9941 0.6007
PSMA6 Layer 5 1.9766 0.5995
TPPP Layer 5 1.9678 0.5984
ETNK1 Layer 4 1.8691 0.5978
RND1 Layer 4 2.1680 0.5977
ATP13A2 Layer 5 2.0039 0.5972

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1506
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1506_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1506/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1506/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1506/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1506/report/PD/BN1506_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1506/report/PD/BN1506_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:33:47
  • Number of Processes: 10
  • Spending Time: 0h 4m